Accept partial payment on manual or draft orders - redux because it was never solved

Payments + Shipping & Fulfilment

Topic summary

Users are frustrated that Shopify still lacks the ability to accept partial payments on manual or draft orders, despite a previous thread being marked as “solved.”

Key Issues:

  • Cannot record deposits or partial payments that differ from the full invoice amount
  • No way to account for external payment methods, exchange rate fluctuations, or payment errors
  • The “Capture order payment” feature only works for exact invoice amounts

Impact:

  • Shopify transaction records don’t reconcile with actual bank deposits
  • Bookkeeping becomes inaccurate and difficult to correct
  • One user reported encountering this problem four times in a single day

Attempted Workarounds Failed:

  • Converting drafts to “pay later” orders and entering partial payments incorrectly marks the entire order as paid
  • No clear way to undo incorrect payment entries

Status: The issue remains unresolved after multiple years, with users calling it a fundamental feature rather than optional functionality.

Summarized with AI on November 1. AI used: claude-sonnet-4-5-20250929.
1

This issue was marked “solved” in another thread. That was a lie, because it was not solved to anybody’s satisfaction.

It’s critical that you actually allow payments to be made that aren’t just the amount for the invoice on manual or draft orders. For example:

  1. Taking a deposit on an invoice and marking it partially paid
  2. To account for external payment mechanisms and the variability of exchange rates (or just user errors)

“Capture order payment” is totally insufficient. There are times where the amount paid is greater than or less than the exact invoice amount. Like, I’ve come across it four times TODAY.

Otherwise, Shopify’s listed transactions just do not reconcile with the bank account and there’s no way to fix it.

No, “buy another subscription app” is not an acceptable response. This is a fundamental feature necessary to keep book keeping correct, not a “nice to have” option.

1 Like
2

This is ridiculous that it hasn’t been solved yet. In one “help” post Shopify says that you mark it “pending”, then apply partial payment and problem solved. This option is not available anywhere on my shopify page in drafts. I converted the draft to an order with “pay later”, then tried to enter partial payment on the real order and it marked the entire order as paid. I have no idea how to undo this as it shows the entire amount paid in Shopify. This is awful for bookkeeping

3

So here we are, another 3 years later, still hasn’t been solved. @Shopify_77 fix your bleep.